3AI8 | pdb_00003ai8

Cathepsin B in complex with the nitroxoline

PDB DOI: https://doi.org/10.2210/pdb3AI8/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-05-11 Released: 2011-05-18
Deposition Author(s): Renko, M., Mirkovic, B., Gobec, S., Kos, J., Turk, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.244 (Depositor), 0.233 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Novel mechanism of cathepsin B inhibition by antibiotic nitroxoline and related compounds

Mirkovic, B., Renko, M., Turk, S., Sosic, I., Jevnikar, Z., Obermajer, N., Turk, D., Gobec, S., Kos, J.

(2011) ChemMedChem 6: 1351-1356

PubMed: 21598397 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.201100098
Primary Citation Related Structures:
3AI8

Organizational Affiliation

Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 56.55 kDa
Atom Count: 4,250
Modeled Residue Count: 512
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin B	A [auth B], B [auth A]	256	Homo sapiens	Mutation(s): 0 Gene Names: CTSB EC: 3.4.22.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07858 (Homo sapiens) Explore P07858 Go to UniProtKB: P07858
PHAROS: P07858 GTEx: ENSG00000164733
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07858
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HNQ Query on HNQ Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	5-nitroquinolin-8-ol C₉ H₆ N₂ O₃ RJIWZDNTCBHXAL-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
HNQ	BindingDB: 3AI8	Ki: min: 3.95e+4, max: 2.72e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.244 (Depositor), 0.233 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.682	α = 90
b = 29.976	β = 126.25
c = 119.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-05-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-01-29
Changes: Database references
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary